For position players, the main difference is how it measures defense. The offensive measure that Baseball Reference uses (OPS+) is generally going to be pretty close to Fangraphs when they use wRC+ and their park factors are similar so we don’t need to worry as much about how they rate hitters. Instead, it’s the defensive difference between using UZR (Fangraphs) and DRS (Baseball Reference) that separates them (again, Baseball Prospectus uses a different stat).
Let’s use Ryan McMahon as an example. He has an fWAR in 2019 of 0.6 and a bWAR of 1.5. When it comes to UZR, Fangraphs ranks him as the 22nd best out of 23 2B in the NL for those who fielded there for at least 300 innings. Among the same fielders, he ranks 7th in terms of DRS.
Now Fangraphs does try to encapsulate both when determining its defensive factor that gets pulled into its WAR formula, but by that measure it still relies heavily on UZR and puts McMahon as the 21st best 2B out of 23. The focus that Baseball Reference puts on DRS certainly factors into why its WAR is nearly 1.0 higher than what Fangraphs calculates.
When using Baseball Reference, always try to keep in mind that it’s probably higher on the Rockies than what you’re going to see on Fangraphs. And if you’re looking at pitchers it’s most likely going to be a little higher than what you see from Baseball Prospectus as well.
It’s generally more friendly to the Rockies and that’s great, but always assume that bWAR can be the potential high point for a Rockies player, especially a pitcher.